X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2bfed88900e97c7c1c04899126e9d1bb56ae1d94;hb=599ce3ebcced809656e12ca0c0f69abd304f1577;hp=3538ff4b1738f95e0516332b803c139306ed7206;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index 3538ff4..2bfed88 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,48 +24,74 @@

- Jalview 2.11 - major and minor new features + Welcome to Jalview Version $$Version-Rel$$ !!

Jalview 2.11 introduces support for loading VCF files, and new - filters and shading models for sequence features. Under the hood, - we've addressed many bugs, and also made some important changes in - the way the Jalview desktop is installed and launched.

VCF Support. Proteins and genomic contigs with - chromosomal location annotation (such as protein coding genes - retrieved from Ensembl) can be annotated with variants imported - from a local VCF file.
The Jalview Launcher and Update System
- Jalview's new installation model means you'll only need to - download and install Jalview once. After installation, Jalview - will automatically keep itself up to date. The launcher also sets - Jalview's memory automatically, so you'll never again have to - manually configure Java's memory settings.
We are grateful to - Install4J who provided us with a free license for their - installation system, and Jalview's over the air update system is - via Getdown.

19 April 2022

Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.

- The full list of bugs fixed in this release can be found in the 2.11 Release Notes. + This release series provides support for two popular 3D + structure visualisation tools, new features for discovery of 3D + structures, improved platform integration and a new command line + tool allowing Jalview to be more easily called from scripts.

+ +

+ View predicted protein structures via 3D-Beacons
+ Jalview 2.11.2's Structure + Chooser includes a client for the 3D-Beacons Network. Launched in + 2021, the 3D-Beacons network (www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/) + provides a central point for the retrieval of predicted and observed + 3D structures for sequences in Uniprot, including homology models + from Swiss-model and deep learning based predictions from the EBI's + Alphafold database (Orengo et al. 2020, doi:10.12688/f1000research.20559.1).

- Jalview and Java 11, 13, and onwards + Support for viewing structures with ChimeraX and + Pymol
Jalview's 3D structure viewer system has been + re-architected to allow easier integration of external structure + viewers, and takes advantage of the strucViz2 Chimera communications + library developed by Scooter Morris (doi:10.1093/bioinformatics/btm329).

+ The Structures + Preferences tab provides new options allowing ChimeraX and + Pymol to be used for visualising external 3D structures. Views + from all structure viewers are saved in Jalview Projects, allowing + them to be shared with others using Jalview 2.11.2 or later, + providing they have the same viewer installed and configured to be + used with Jalview.

Jalview + 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2 + (incentive). For ChimeraX, we recommend using v1.3 or later.

Java 11 provides improved performance and better OS - integration, so we now recommend users select our Java 11 Jalview - distribution rather than the legacy Java 8 build.

- Known Issues - update for 211 +

Other highlights include:

OSX: The 'Open File' dialog for Jalview's Groovy Console - appears with the title 'Save As', and attempting to select a file - to load yields a FileNotFound exception.
The workaround is to first - clear the 'Untitled' filename before selecting the file you wish - to load. +
Import of annotated DNA and RNA loci via GenBank and EMBL + style flatfile
Easier configuration of Jalview's memory + allocation
Scripts for running + Jalview via the command line on macOS, Linux/Unix and Windows.
OSX: Links don't open when clicked on or via the Sequence - or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items

+ + +

+ For the full details, see the Jalview 2.11.2.1 + release notes. +

+ Known Issues
The following known issues will + be addressed in a minor patch release. + +

Display of RESNUM sequence features are not suppressed when + structures associated with a sequence are viewed with an external + viewer (Regression from 2.11.1 series)